RNA Modification

Abstract

Naturally occurring ribonucleic acids (RNAs) contain over 150 chemically altered nucleosides formed by enzymatic modification of the primary RNA transcript during the complex tRNA maturation process. This post‐transcriptional RNA modification is a universally conserved and highly complex metabolic process in the living cell. Cellular RNAs are modified by pure protein stand‐alone enzymes, as well as by s(sno)RNP complexes containing guide s(sno)RNAs. Modified nucleotides present in RNA play an important role in stabilisation of 2D and 3D structures of these molecules, as well as in the fine‐tuning of numerous interactions between RNAs itself and with RNA‐binding protein partners. Modification also protects RNAs against nucleolytic degradation and improves their performance in different interactions in which various RNAs are involved. For example, modifications present in the tRNA anticodon loop are crucially important for correct mRNA decoding during the protein synthesis on the ribosome. Recent progress in the field points out the regulatory character of RNA modification. This emerging concept of ‘RNA‐epigenetics’ supplies the additional level to the regulation of gene expression. This regulation (and deregulation) of RNA‐modification machineries is a basis for some important human pathologies.

Key Concepts

  • Cellular RNAs are post‐transcriptionally modified in all life kingdoms
  • RNA modification alters physico‐chemical properties of nucleotides, including their conformation, polarity, hydrophobicity, chemical reactivity and base‐pairing interactions
  • RNA modification is performed by highly specific and regulated enzymatic mechanisms involving pure protein enzymes and catalytic RNA–protein complexes (RNPs)
  • RNA modification is important for regulation of gene expression
  • Transcription‐wide RNA modification is dynamic and regulated cellular process
  • Deregulation of RNA modification may lead to important human pathologies

Keywords: modified nucleotides; methylation; thiolation; pseudouridine; anticodon; mRNA decoding

Figure 1. Types of chemical alterations and their location within the purine and pyrimidine derivatives in all kinds of RNAs (tRNA, rRNA, mRNA, snRNA, etc.) from various organisms. The groups that differentiate from the canonical A, G, C or U are in red. Base positions are numbered in blue (conventional numbering for purine and pyrimidine rings). In naturally occurring RNAs, various combinations of different modifications exist, thus extending the total number of the modified nucleosides present in RNAs over 140. Modified A and inosine (I) nucleotides (a), G nucleotides (b), 2′‐O‐modifications (c), modified C residues (d), modified U and Ψ derivatives (e) and 7‐deaza and queuosine (Q) derivatives (f). Except for 7‐deazaguanosine and queuosine derivatives, the purine and pyrimidine ring (in black) are those initially encoded in RNA during transcription. For more details about the chemistry and occurrence of modified nucleosides in RNA, see (Sprinzl et al., ) or (Cantara et al., ).
Figure 2. Phylogenetic distribution of modified nucleosides in RNA originating from the three domains of life. Abbreviations of modified nucleosides are as in Figure. Data presented in this figure may be in contradiction with other sources owing to: (1) limited information available on the RNA sequence of many Archaea RNAs, (2) discrepancies between direct tRNA sequencing data and global nucleoside composition analysis by HPLC‐MS and (3) errors, misinterpretation or misidentification of modified residues in tRNA molecules. Compilation was performed using RNA‐modification database and MODOMICS database (Cantara et al., ; Czerwoniec et al., ).
Figure 3. (a) Wire structure of C/D and H/ACA‐box snoRNAs. The conserved sequences (boxes C/D and C′/D′ in C/D snoRNA and H and ACA boxes in H/ACA snoRNA) are indicated. (b) Schematic representation of the assembled C/D sRNPs structure obtained by NMR, adapted from Lapinaite et al., (). sno(s)RNA guide is shown in orange, the substrate RNA in red, and positions of conserved proteins of C/D particle (Nop5, fibrillarin (Fib) and L7ae) are defined on the basis of high‐resolution structure. Conserved sequences of Boxes D′ in sRNA are indicated. (c) Schematic representation of H/ACA s(sno)RNP particles, the expected locations of snoRNP proteins are indicated. Adapted with permission from Wang, C. and Meier, U.T. (2004). © European Molecular Biology Organization.
Figure 4. Cellular localisation of RNA:modification enzymes and coordination between RNA (tRNA) maturation and modification. The scheme describes in detail the maturation of eukaryotic tRNAs, but may also be generalised to other RNA molecules. Transcription of RNA genes happens in the nucleus, and after short initial folding, RNA‐modification enzymes modify these nascent RNA transcripts (early nuclear modifications). Maturation proceeds by 5′‐ and 3′‐trimming and concomitant action of other components of RNA‐modification machinery (late nuclear modifications). Some RNAs transit through the nucleolus and are modified there by snoRNA RNPs (C/D and H/ACA). tRNA introns are spliced at the level of nuclear pore, and almost mature tRNAs are released to the cytoplasm, where some additional (late cytoplasmic) modifications take place. Eukaryotic mitochondrial tRNAs are mostly produced inside the mitochondria and modified there by imported RNA:modification enzymes. In some instances tRNAs are further imported from the cytoplasm to the organelles (mitochondria and chloroplasts).
Figure 5. Major concepts of RNA (tRNA) recognition by RNA:modification enzymes. (a) Identity elements (specific nucleotides indicated by orange dots) insure recognition of unique (or few RNA substrates). (b) Recognition of global 3D architecture of the RNA molecule, 3D tRNA core is indicated in red and overall 3D structure is outlined in dark blue. (c) Recognition of local structural domain which may be present in different RNA molecules. Anticodon stem‐loop and Tψ‐stem‐loop are highlighted in green and orange, respectively. (d) Concept of separate RNA guide to govern RNA‐substrate recognition. Target RNA does not contain any identity element and the enzyme recognises the duplex formed by target RNA and RNA guide (example of s(sno)‐RNA‐guided 2′‐O‐methylathion). In this case the guide contains the recognised sequence.
Figure 6. Modification alters physico‐chemical and base‐pairing properties of nucleotides. Examples of modified residues derived from A (a), G (b), C (c) and U (d). Additional chemical groups are shown in red and parental nucleotide in black. Modified nucleotide m7G (b) specifically reacts with NaBH4, m5C (C) is not deaminated by Na2SO3, compared to unmodified C. Pseudouridine (d) reacts with soluble carbodiimides such as CMCT, s2U with organomercuric substances and 2′‐O‐Me groups bring resistance to alkaline cleavage. Other modifications affect hydrophobicity, conformation (Ψ and D (d)) and base‐pairing properties.
Figure 7. Known functions of RNA modification. The presence of modified residues in RNA: affects the overall thermostability of RNA molecules (a), adapted with permission from Cabello‐Villegas, J. and Nikonowicz, E.P. (). © Oxford University Press, or affects their resistance to endonuclease cleavages (case of 2′‐O‐Me) (b) and modulates the antibiotic resistance of bacteria by appropriate rRNA modification (c), adapted from Wilson, D.N. (). © Nature Publishing Group. Modified residues also modulate the tRNA recognition by TLR7 receptors and thus modulate immune response (d), adapted from Hori, H. () and affect recognition of tRNAs and other RNAs by specific proteins (e), adapted from Suzuki, T. and Miyauchi, K. (). © Elsevier. At the level of translation, modified nucleotides in tRNA and in mRNA affect codon–anticodon recognition and thus mRNA decoding by the ribosome (f) (PDB structure 1XMO, tRNALys(UUU)), modulate frameshifting efficiency (g). Finally, widespread modification of mRNAs in eukaryotic cells (m6A and Ψ) is supposed to control gene expression (h) Liu et al. ().
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References

Agris PF (1996) The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. Progress in Nucleic Acid Research and Molecular Biology 53: 79–129.

Agris PF (2004) Decoding the genome: a modified view. Nucleic Acids Research 32: 223–238.

Agris PF, Vendeix FAP and Graham WD (2007) tRNA's wobble decoding of the genome: 40 years of modification. Journal of Molecular Biology 366: 1–13.

Allnér O and Nilsson L (2011) Nucleotide modifications and tRNA anticodon‐mRNA codon interactions on the ribosome. RNA 17: 2177–2188.

Bachellerie JP, Cavaillé J and Hüttenhofer A (2002) The expanding snoRNA world. Biochimie 84: 775–790.

Baker DL, Youssef OA, Chastkofsky MIR, et al. (2005) RNA‐guided RNA modification: functional organization of the archaeal H/ACA RNP. Genes and Development 19: 1238–1248.

Behm‐Ansmant I, Helm M and Motorin Y (2011) Use of specific chemical reagents for detection of modified nucleotides in RNA. Journal of Nucleic Acids 2011: 408053.

Boschi‐Muller S and Motorin Y (2013) Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification. Biochemistry (Mosc) 78: 1392–1404.

Cabello‐Villegas J and Nikonowicz EP (2005) Solution structure of psi32‐modified anticodon stem‐loop of Escherichia coli tRNAPhe. Nucleic Acids Research 33: 6961–6971.

Cantara WA, Crain PF, Rozenski J, et al. (2011) The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Research 39: D195–D201.

Carlile TM, Rojas‐Duran MF, Zinshteyn B, et al. (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515: 143–146.

Cavaillé J, Nicoloso M and Bachellerie JP (1996) Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383: 732–735.

Chan CTY, Pang YLJ, Deng W, et al. (2012) Reprogramming of tRNA modifications controls the oxidative stress response by codon‐biased translation of proteins. Nature Communications 3: 937.

Czerwoniec A, Dunin‐Horkawicz S, Purta E, et al. (2009) MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Research 37: D118–D121.

Decatur WA and Fournier MJ (2003) RNA‐guided nucleotide modification of ribosomal and other RNAs. Journal of Biological Chemistry 278: 695–698.

Edelheit S, Schwartz S, Mumbach MR, Wurtzel O and Sorek R (2013) Transcriptome‐wide mapping of 5‐methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genetics 9: e1003602.

Ferré‐D'Amaré AR (2003) RNA‐modifying enzymes. Current Opinion in Structural Biology 13: 49–55.

Gustilo EM, Vendeix FA and Agris PF (2008) tRNA's modifications bring order to gene expression. Current Opinion in Microbiology 11: 134–140.

Hori H (2014) Methylated nucleosides in tRNA and tRNA methyltransferases. Frontiers in Genetics 5: 144.

Isel C, Marquet R, Keith G, Ehresmann C and Ehresmann B (1993) Modified nucleotides of tRNA(3Lys) modulate primer/template loop‐loop interaction in the initiation complex of HIV‐1 reverse transcription. Journal of Biological Chemistry 268: 25269–25272.

Iwata‐Reuyl D (2008) An embarrassment of riches: the enzymology of RNA modification. Current Opinion in Chemical Biology 12: 126–133.

Jia G, Fu Y and He C (2013) Reversible RNA adenosine methylation in biological regulation. Trends in Genetics 29: 108–115.

Kawai G, Ue H, Yasuda M, et al. (1991) Relation between functions and conformational characteristics of modified nucleosides found in tRNAs. Nucleic Acids Symposium Series 25: 49–50.

Lane BG (1998) Historical perspectives on RNA nucleotide modifications. In: Grosjean H and Benne R, (eds). The Modification and Editing of RNA, pp. 1–20. New York, NY: ASM Press.

Lapinaite A, Simon B, Skjaerven L, et al. (2013) The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature 502: 519–523.

Liu J, Yue Y, Han D, et al. (2014) A METTL3‐METTL14 complex mediates mammalian nuclear RNA N6‐adenosine methylation. Nature Chemical Biology 10: 93–95.

Marshak‐Rothstein A (2006) Toll‐like receptors in systemic autoimmune disease. Nature Reviews Immunology 6: 823–835.

Massenet S, Mougin A and Branlant C (1998) Posttranscriptional modifications in the U small nuclear RNAs. In: Grosjean H and Benne R, (eds). The Modification and Editing of RNA, pp. 201–227. New York, NY: ASM Press.

Mitchell JR, Wood E and Collins K (1999) A telomerase component is defective in the human disease dyskeratosis congenita. Nature 402: 551–555.

Motorin Y, Muller S, Behm‐Ansmant I and Branlant C (2007) Identification of modified residues in RNAs by reverse transcription‐based methods. Methods in Enzymology 425: 21–53.

Motorin Y and Helm M (2011) RNA nucleotide methylation. Wiley Interdisciplinary Reviews. RNA 2: 611–631.

Nelson ND and Bertuch AA (2012) Dyskeratosis congenita as a disorder of telomere maintenance. Mutation Research 730: 43–51.

Niu Y, Zhao X, Wu Y‐S, et al. (2013) N6‐methyl‐adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics, Proteomics & Bioinformatics 11: 8–17.

Patil A, Chan CTY, Dyavaiah M, et al. (2012) Translational infidelity‐induced protein stress results from a deficiency in Trm9‐catalyzed tRNA modifications. RNA Biology 9: 990–1001.

Rozenski J, Crain PF and McCloskey JA (1999) The RNA Modification Database: 1999 update. Nucleic Acids Research 27: 196–197.

Saletore Y, Chen‐Kiang S and Mason CE (2013) Novel RNA regulatory mechanisms revealed in the epitranscriptome. RNA Biology 10: 342–346.

Schwartz S, Bernstein DA, Mumbach MR, et al. (2014) Transcriptome‐wide mapping reveals widespread dynamic‐regulated pseudouridylation of ncRNA and mRNA. Cell 159: 148–162.

Shigi N, Sakaguchi Y, Suzuki T and Watanabe K (2006) Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures. Journal of Biological Chemistry 281: 14296–14306.

Spenkuch F, Motorin Y and Helm M (2015) Pseudouridine: Still mysterious, but never a fake (uridine)!. RNA Biology 11 (12): 1540–1554.

Sprinzl M, Grueter F, Spelzhaus A and Gauss DH (1980) Compilation of tRNA sequences. Nucleic Acids Research 8: r1–r22.

Suzuki T, Suzuki T, Wada T, Saigo K and Watanabe K (2002) Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO Journal 21: 6581–6589.

Suzuki T and Miyauchi K (2010) Discovery and characterization of tRNAIle lysidine synthetase (TilS). FEBS Letters 584: 272–277.

Umeda N, Suzuki T, Yukawa M, et al. (2005) Mitochondria‐specific RNA‐modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases. Journal of Biological Chemistry 280: 1613–1624.

Vester B and Long KS (2000) Antibiotic resistance in bacteria caused by modified nucleosides in 23S Ribosomal RNA. In: Grosjean H, (ed). DNA and RNA Modification Enzymes: Structure, Mechanism and Evolution. Austin: Landes Bioscience.

Vinayak M and Pathak C (2010) Queuosine modification of tRNA: its divergent role in cellular machinery. Bioscience Reports 30: 135–148.

Wang C and Meier UT (2004) Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. EMBO Journal 23: 1857–1867.

Wei F‐Y, Suzuki T, Watanabe S, et al. (2011) Deficit of tRNA(Lys) modification by Cdkal1 causes the development of type 2 diabetes in mice. Journal of Clinical Investigation 121: 3598–3608.

Wilson DN (2014) Ribosome‐targeting antibiotics and mechanisms of bacterial resistance. Nature Reviews Microbiology 12: 35–48.

Yarian C, Townsend H, Czestkowski W, et al. (2002) Accurate translation of the genetic code depends on tRNA modified nucleosides. Journal of Biological Chemistry 277: 16391–16395.

Zeharia A, Fischel‐Ghodsian N, Casas K, et al. (2005) Mitochondrial myopathy, sideroblastic anemia, and lactic acidosis: an autosomal recessive syndrome in Persian Jews caused by a mutation in the PUS1 gene. Journal of Child Neurology 20: 449–452.

Further Reading

Grosjean H and Benne R (eds) (1999) The Modification and Editing of RNA. New York, NY: ASM Press.

Grosjean H (ed) (2009) DNA and RNA Modification Enzymes: Structure, Mechanism and Evolution. Austin: Landes Bioscience.

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Motorin, Yuri(May 2015) RNA Modification. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000528.pub3]